Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation.

Cells integrate exogenous and endogenous signals to grow, repair, or die. This is likely achieved through dynamic functional associations between genes, but measuring these relationships at scale is non-trivial. Here, we evaluate genetic associations in response to cell-cycle interruption, genotoxic perturbation, and nutrient deprivation using conditional genetic interaction (GI) mapping in human cells. In five maps measuring ∼250,000 GIs or higher-order environmental interactions, we discover widespread rewiring of relationships between genes, complexes, and ontologies across conditions. Specific bioprocesses drive the rewiring signal in each environmental state, as highlighted in our findings that the TIP60 and PP2A complexes radically alter their interaction profiles after inhibition of ATR. This resource reveals numerous genetic relationships for the fields of DNA damage signaling, DNA repair, and cell-cycle control and explores their context specificity. Our work advances a framework for using GI maps to explore environmental rewiring.